tag:blogger.com,1999:blog-37148773.post4277928531153523363..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Definitions Matter: Negative Selection and Postive SelectionLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger24125tag:blogger.com,1999:blog-37148773.post-14388414571480303782011-11-07T23:25:32.249-05:002011-11-07T23:25:32.249-05:00If two beneficial alleles compete, which one would...If two beneficial alleles compete, which one would be positive or negative? Is it a relative term?seannoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-27897680402939289922008-10-29T17:19:00.000-04:002008-10-29T17:19:00.000-04:00Yes. Finally you understood it. Yes, you are not l...Yes. Finally you understood it. Yes, you are not living in the water because there will be a very strong negative selection against your there. And you are not living on another planet that is just like Earth because the environment exerts a strong negative selection against you getting there - you are not adapted enough to reach that planet to begin with.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-3426332382083126962008-10-29T17:05:00.000-04:002008-10-29T17:05:00.000-04:00so, we are under negative selection for nay enviro...so, we are under negative selection for nay environment we don't live in?<BR/>I am under negative selection for living in water, for instance.<BR/><BR/>Hehehehehe<BR/><BR/>Take care now. Byebye thenA. Vargashttps://www.blogger.com/profile/04876504431768677209noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-87307758877983098792008-10-29T16:09:00.000-04:002008-10-29T16:09:00.000-04:00Sure as hell it's still a selection. The other guy...Sure as hell it's still a selection. The other guys couldn't live in the new environment because of the negative selection pressure exerted on them by that environment (otherwise they would be living there, a no brainer!)<BR/><BR/>So the mutated guys who managed to survive there were positively selected.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-36297265116983315522008-10-29T14:03:00.000-04:002008-10-29T14:03:00.000-04:00If you are going to use the word "selection" then ...If you are going to use the word "selection" then you have to talk about a "selective pressure" affecting different phenotypes in the same population. <BR/>What is the selective pressure in that example? Is selection being applied to a single population, if part of the population cannot even live in the same environment?<BR/><BR/>I cannot agree with you calling that "selection".<BR/><BR/>If anything, the mutation is selecting the environment, and not the other way round.<BR/><BR/>Another question. Are you aware that most people would call the peppered moth case a simple case of negative selection (elimination of the white moths)<BR/><BR/>To call it "positive selection", selection should have a role in the generation of a new phenotype, not just the elimination of another.<BR/><BR/>But you would call that "positive selection for black moths".<BR/><BR/>In fact, in your book, negative selection always implies there is "positive selection"....of whoever is not being eliminated. Hehe. You can ALWAYS find positive selection!!!<BR/><BR/>Mushy? <BR/>Indeed.A. Vargashttps://www.blogger.com/profile/04876504431768677209noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-57470429143080846512008-10-29T13:22:00.000-04:002008-10-29T13:22:00.000-04:00So, when a new mutation colonizes a new environmen...<I> So, when a new mutation colonizes a new environment, it founds a new population without outcompeting its population of origin. In this new, growing population everyone is as fit as the next.<BR/><BR/>Is that positive selection? </I> <BR/><BR/>If that new mutation ALLOWED colonization of the new environment then yes, it is undoubtedly a positive selection. More places to propagate = higher fitness.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10987536713479043932008-10-29T12:57:00.000-04:002008-10-29T12:57:00.000-04:00"Saying that "positive selection "creates the fit"..."Saying that "positive selection "creates the fit" is a vague statement that is of no value to me"<BR/><BR/>Well, you should care, because it is still quite mainstream to say that negative selection merely eliminates the unfit, whereas it is positive selection that has an active role in the origin of adaptations. This is my main beef with people ts tossing around the notion of "positive selection" <BR/><BR/>"It is what happens in nature when a trait confers increase in fitness"<BR/><BR/><BR/>That's a fairly good definition, but keep in mind that fitness is relative to the rest of the population. <BR/><BR/>So, when a new mutation colonizes a new environment, it founds a new population without outcompeting its population of origin. In this new, growing population everyone is as fit as the next. <BR/><BR/>Is that positive selection?A. Vargashttps://www.blogger.com/profile/04876504431768677209noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-66005877475534643202008-10-29T12:39:00.000-04:002008-10-29T12:39:00.000-04:00This comment has been removed by the author.A. Vargashttps://www.blogger.com/profile/04876504431768677209noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-21921003098145011812008-10-29T12:20:00.000-04:002008-10-29T12:20:00.000-04:00I don't want to read a little on how others define...I don't want to read a little on how others define positive selection. Here is my definition of positive selection: <BR/><BR/>It is what happens in nature when a trait confers increase in fitness. <BR/><BR/>Saying that "positive selection "creates the fit" is a vague statement that is of no value to me.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-88381756558233350742008-10-29T10:01:00.000-04:002008-10-29T10:01:00.000-04:00You need to read up a little on definitions of pos...You need to read up a little on definitions of positive selection. Some authors argue that positive selection "creates the fit" while negative selection "eliminates the unfit"<BR/>What do you think of that?A. Vargashttps://www.blogger.com/profile/04876504431768677209noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-89105463960048858752008-10-29T09:59:00.000-04:002008-10-29T09:59:00.000-04:00So, if I understand, in your definition positive s...So, if I understand, in your definition positive selection = adaptation, and vice-versa. <BR/><BR/>What do you think about my argument of a mutation that colonizes a new environment without outcompeting its population of origin? <BR/><BR/>Adaptationists are usually strangely deaf to that argumentA. Vargashttps://www.blogger.com/profile/04876504431768677209noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-20655149138052309502008-10-29T09:23:00.000-04:002008-10-29T09:23:00.000-04:00To a. vargas and Larry:Of course not. What I wrote...To a. vargas and Larry:<BR/><BR/>Of course not. What I wrote refers to SELECTION. So IF there is a selection, the direction is straightforward. That's what I meant. In the case of Y. pestis, the mutation is clearly adaptive, not neutral.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-22810485835353192592008-10-29T09:12:00.000-04:002008-10-29T09:12:00.000-04:00DK says,Increase in frequency = positive selection...DK says,<BR/><BR/><I>Increase in frequency = positive selection. Decrease = negative. Anything more simple than this</I><BR/><BR/>An allele could increase in frequency in a population by random genetic drift. Similarly, an allele can decrease by random genetic drift.<BR/><BR/>Is that what you call "simple"?<BR/><BR/>Your definitions are incorrect.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-51596662258829472342008-10-29T06:00:00.000-04:002008-10-29T06:00:00.000-04:00Since it is online, have the manuscript corrected ...Since it is online, have the manuscript corrected noting the past version, the error and the letter exchange. This can be denoted as well in the PDF version. The error is corrected and a constant reminder is in place for the editor, reviewers and authors of their serious error.PonderingFoolhttps://www.blogger.com/profile/10767758746935185528noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-1051066070734757642008-10-29T00:44:00.000-04:002008-10-29T00:44:00.000-04:00"Increase in frequency = positive selection. Anyth..."Increase in frequency = positive selection. Anything more simple than this?"<BR/><BR/>Hehehe. <BR/><BR/>Given you made such simple requirements a gene that increases its frequency by a foundation effect or a bottleneck fully qualifies as an example of "positive selection". <BR/><BR/>Where's the good ole darwinian "betterment" there? Where's the competition? <BR/><BR/>Seems like you'll have to elaborate.<BR/>Tip: there's no way around discussing a correspondence of phenotype to environment.<BR/><BR/>I insist: What has happened in the evolution of Yersinia is not at all necessarily best described as "positive selection". <BR/><BR/>Indeed, I find the argument to be typical: Point your finger to any adaptation and just say "positive selection". Works like a charm.A. Vargashttps://www.blogger.com/profile/04876504431768677209noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-47297942026446415212008-10-28T20:53:00.000-04:002008-10-28T20:53:00.000-04:00Woa, a single post evoking a panoply of problems i...Woa, a single post evoking a panoply of problems in modern biology. <BR/><BR/>People doing useful and successful science without understanding the basic tenets of the subject? - Check. <BR/><BR/>Publishing in PNAS the old corrupt way? - Check. <BR/><BR/>Failure of peer review? - Check. <BR/><BR/>Too much bullshit published and going unnoticed? - Check. <BR/><BR/>The answer to the question Larry posed in the end: <BR/><BR/>PNAS and the authors have to have the guts to retract the paper and publish a new one with the basic error corrected. An erratum or corrigendum won't cut it in such a case. <BR/><BR/>DKAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-74026386825807594742008-10-28T20:42:00.000-04:002008-10-28T20:42:00.000-04:00The term "positive selection" is a mushy term Not...<I> The term "positive selection" is a mushy term </I> <BR/><BR/>Nothing mushy about it. Or, to be super precise, it is as much mushy as any perfectly common term. That some people who have no clue use it loosely does not make it mushy (cf. "liberal"). <BR/><BR/>Increase in frequency = positive selection. Decrease = negative. Anything more simple than this?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-74801798556671127982008-10-28T20:08:00.000-04:002008-10-28T20:08:00.000-04:00The title can certainly be changed, as an erratum....The title can certainly be changed, as an erratum. It happened to a colleague of mine in the same journal:<BR/><BR/>Du W, Maniatis T. "An ATF/CREB binding site is required for virus induction of the human interferon beta gene [corrected]" <I>Proc Natl Acad Sci USA.</I> 1992 Mar 15;89(6):2150-4. Erratum in: <I>Proc Natl Acad Sci USA</I> 1992 Jun 15;89(12):5700.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-72399016881617514282008-10-28T19:35:00.000-04:002008-10-28T19:35:00.000-04:00The term "positive selection" is a mushy term, so ...The term "positive selection" is a mushy term, so it's funny that Larry would complains about it as if it were carved into stone, with a precise meaning . No sir. <BR/><BR/>For instance, "positive selection" has been used for sequences that have a greater rate of translated vs neutral (3rd codon) substitutions. <BR/><BR/>Or, it is used to connote a "creative" or "shaping" role of selection (rather than simply making an available trait more frequent).A. Vargashttps://www.blogger.com/profile/04876504431768677209noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35183448428900199172008-10-28T19:15:00.000-04:002008-10-28T19:15:00.000-04:00Devin asks,As long as people are clear on what the...Devin asks,<BR/><BR/><I>As long as people are clear on what the authors meant, is their error really that important?</I><BR/><BR/>Let's say you're looking for good examples of positive selection in natural populations of bacteria.<BR/><BR/>Would you find this article in a PubMed search?<BR/><BR/>I think it matters on many levels. We try to teach our students how to think critically and part of that process means defining your terms. This paper seems to be an example of very fuzzy thinking.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-72546258815317243492008-10-28T19:03:00.000-04:002008-10-28T19:03:00.000-04:00Would it be possible to change the title? "Experim...Would it be possible to change the title? "Experimental evidence for positive selection (formerly negative selecton)"?Monadohttps://www.blogger.com/profile/12523329434641725631noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10906380978351441712008-10-28T14:53:00.000-04:002008-10-28T14:53:00.000-04:00There are links to the commentary on the PNAS onli...There are links to the commentary on the PNAS online version of the article.<BR/>As long as people are clear on what the authors meant, is their error really that important?Devinhttps://www.blogger.com/profile/01119444616659234057noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-85812803982635859672008-10-28T14:50:00.001-04:002008-10-28T14:50:00.001-04:00This comment has been removed by the author.A. Vargashttps://www.blogger.com/profile/04876504431768677209noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-82124597999685979432008-10-28T14:50:00.000-04:002008-10-28T14:50:00.000-04:00You exaggerate to shred your inner garments over ...You exaggerate to shred your inner garments over the state of "modern science".<BR/><BR/>Why? First, the work describes an interesting case well enough, which remains interesting, regardless of what yo may call it.<BR/><BR/>Second, because "positive selection" IS a murky an largely abused notion. I think there is an epistemological problem there, such that almost anything can end up being described as "positive selection" ultimately based on good ole adaptationist thinking and "darwinistic" bias.<BR/><BR/>For instance, when we call this "positive selection", we imagine a scenario where a given mutant bacterium gets and advantage in the population; it is "better", outcompeting other less fit bacteria. However, this scenario requires us to imagine a<BR/>population that, despite living in fleas, cannot infect that good because it carries a harmful gene; in other words, we must assume the population goes through an initial "live like shit" phase. Weird, huh? <BR/><BR/>Is this realistic? Do these people even conceive of the possiblity that the entire initial population is NOT living like shit, but in some other lifestyle? Film-making mutants have the possibility of colonizing new environments, such as fleas. In this scenario, the pseudogenizing mutation is initially neutral; it allows colonization of the flea, which is like a founder effect. Colonizing a new environment is quite a different thing from outcompeting the population of origin... Further, in this new environment, going back to the functional mutation is, without doubt, negatively selected.<BR/><BR/>So, competitive positive selection? or drift, colonization and negative selection? At least to me this is not a matter of simply applying definitions as if these were delivered by nature itself. I think there is a genuine problem here.A. Vargashttps://www.blogger.com/profile/04876504431768677209noreply@blogger.com